Combining image / panoramic

[GloryField]

Hi all,

Taking a picture of the cross-section of a nerve at 200x shows the entire nerve, but the axons/fibers are too small to be seen/counted.  So what I would like to do is take 4 separate pictures of the 4 quadrants of the nerve at 400x, and then be able to combine them into a single image.  Is there a way in imageJ to automatically account for the overlap of the 4 images?

Thank you

[edsimmons]

GloryField wrote

Hi all,

Taking a picture of the cross-section of a nerve at 200x shows the entire nerve, but the axons/fibers are too small to be seen/counted.  So what I would like to do is take 4 separate pictures of the 4 quadrants of the nerve at 400x, and then be able to combine them into a single image.  Is there a way in imageJ to automatically account for the overlap of the 4 images?

Thank you

Hi,

Does this look helpful?

http://bigwww.epfl.ch/thevenaz/mosaicj/

I plan to try this myself soon, but haven't yet used it. I'd be glad to hear how you get on.

Best,
Ed

[Albert Cardona-2]

2011/10/7 edsimmons <[hidden email]>:

> GloryField wrote:
>>
>> Hi all,
>>
>> Taking a picture of the cross-section of a nerve at 200x shows the entire
>> nerve, but the axons/fibers are too small to be seen/counted.  So what I
>> would like to do is take 4 separate pictures of the 4 quadrants of the
>> nerve at 400x, and then be able to combine them into a single image.  Is
>> there a way in imageJ to automatically account for the overlap of the 4
>> images?

Stitching plugin for images or stacks (translation only):
  http://fiji.sc/wiki/index.php/Stitching_2D/3D

TrakEM2 plugin for montages (from translation only to elastic registration):
  http://fiji.sc/wiki/index.php/TrakEM2
(see for example: http://fiji.sc/wiki/index.php/File:Trakem2-snap.jpg )

Hope that helps.

Albert

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

[Rainer Kohler-2]

Hi,

Fiji has stitching plugin that works well to combine overlapping images.


Rainer

On 10/7/11 9:01 AM, edsimmons wrote:

> GloryField wrote:
>> Hi all,
>>
>> Taking a picture of the cross-section of a nerve at 200x shows the entire
>> nerve, but the axons/fibers are too small to be seen/counted.  So what I
>> would like to do is take 4 separate pictures of the 4 quadrants of the
>> nerve at 400x, and then be able to combine them into a single image.  Is
>> there a way in imageJ to automatically account for the overlap of the 4
>> images?
>>
>> Thank you
>>
> Hi,
>
> Does this look helpful?
>
> http://bigwww.epfl.ch/thevenaz/mosaicj/
>
> I plan to try this myself soon, but haven't yet used it. I'd be glad to hear
> how you get on.
>
> Best,
> Ed
>
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Combining-image-panoramic-tp6867276p6869227.html
> Sent from the ImageJ mailing list archive at Nabble.com.

... [show rest of quote]

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[GloryField]

thank you all, I tried the stitching directory with unknown configuration in FIJI and it worked great!

[GloryField]

Another question about using the analyze particles in ImageJ/FIJI

here's a sample image I made using stitching:
http://www.swapdrive.com/file.asp?ID=tG+4c+dQUV2uaBUzGE9QXIqvYD6NpPr0zU3HMp4maEzHuo55/04pqQ==url

I'm trying to measure the average area of each of the axons within the nerve, including the myelin sheath.

What I did so far is:
Process>Subtract Background>5 pixels
Process>Binary>Make Binary
Analyze>Analyze Particles>Size 4-350, circularity 0.25-1.0, show outlines, include holes

I chose 350 as max size because that allows me to eliminate blood vessels within the nerve.
I arbitrarily chose 0.25 circularity because I didn't know what else to pick.

Doing this gave me an average size of 50.668 pixels.  I will put a slide with a length marker under microscope with same magnification so I can use "Analyze > Set Scale" and get values in micrometers.

Do you guys think this would be an OK way of measuring the axon cross section area?

Thank you again!